Post-doctoral Fellow

National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

present - 2020

Research Associate

National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

2022 - 2020

PhD., Crop Genetics and Breeding

Huazhong Agricultural University

Wuhan, CN

2019 - 2014

• Thesis: Reference-level Genome Assembly of Black pepper and Molecular Basis Study of Piperine Biosynthesis

Bachelor of Agriculture

Tianjin Agricultural University

Tianjin, CN

2014 - 2010

• Thesis:

博士研究生国家奖学金

N/A

华中农业大学

2016

第二届傅家瑞青年种子生物学优秀研究论文二等奖

N/A

华中农业大学

2017

优秀博士生资助计划

N/A

华中农业大学

第十二届长三角作物学博士论坛优秀奖

N/A

华中农业大学

2018

第二届武汉•南湖作物学与植物保护博士生论坛三等奖

N/A

华中农业大学

2019

2019~2020学年校研究生优秀学位论文

N/A

华中农业大学

2020 - 2019

植物科学技术学院优秀博士后资助

Huazhong Agricultural University

N/A

present - 2020

Background of biological research

I possess a strong knowledge base in the field of biology, having successfully completed foundational courses including Plant Biotechnology, Genomics, Molecular Biology, and Plant Physiology. Furthermore, I have developed proficiency in various experimental techniques, such as cotton transgenic technology, southern hybridization and other biology experimental skills related molecular.

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Bioinformatics analysis capabilities

N/A

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• Familiar with the analysis methods of high-throughput sequencing data, with practical experience in the assembly, annotation, and biological mining of complex genomes such as diploid and polyploid, as well as data analysis related to RNA-seq, Resequencing, ATAC-seq, ChIP-seq, and CRISPR genome editing;
• Proficient in using the Linux system as a platform for bioinformatics data analysis tasks;
• Proficient in configuring and deploying large-scale computing tasks using Linux clusters;
• Proficient in programming languages such as Python, R, and Shell;
• Proficient in programming languages such as Python, R, and Shell;
• Having in-depth research on the utilization and algorithm principles of multiple mainstream bioinformatics software;

Literature Reading and Writing Skills

I have developed strong skills in reading, classifying, organizing, and summarizing of literature, enabling to effectively navigate and comprehend scientific research literatures. Furthermore, I possess proficient writing skills for SCI paper publication, ensuring that effectively communicate research findings in a clear and concise manner.

N/A

CSEF基因调控棉花体细胞胚胎发生的分子机制研究 (32201856)

主持, CNY ￥300,000, 国家自然科学基金, 青年基金

N/A

2025 - 2023

中黑盲蝽效应子的筛选与功能研究

主持, CNY ￥50,000, 湖北省自然科学基金, 青年项目

N/A

2024 - 2022

水稻、棉花等基因编辑作物创制及分子特征检测技术

主持, CNY ￥2,418,000,农业生物育种重大项目, 农业农村部科技发展中心

N/A

2025 - 2022

农业生物重要性状形成与环境适应性基础研究

主持, CNY ￥700,000,国家重点研发计划, 中华人民共和国科学技术部

N/A

2027 - 2022

具有我国自主知识产权的新型基因编辑系统的开发与利用 (2021hszd013)

参与, CNY ￥2,000,000, 湖北洪山实验室

N/A

2025 - 2022

基因编辑驱动的基因定向进化创制抗除草剂棉花及单倍体诱导 (B21HJ8103)

参与, CNY ￥400,000, 海南省崖州湾种子实验室

N/A

2013

多倍体作物转录调控网络演化与性状形成

参与, CNY ￥2,000,000, 国家重点研发计划, 中华人民共和国科学技术部

N/A

2025 - 2022

Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem

Genome Biology. 2023, 24, 194.

N/A

2023

• Xiangqian Zhu^#, Zhongping Xu^#, Guanying Wang, Yulong Cong, Lu Yu, Ruoyu Jia, Yuan Qin, Guangyu Zhang, Bo Li, Daojun Yuan, Lili Tu, Xiyan Yang, Keith Lindsey, Xianlong Zhang^*, Shuangxia Jin^*

Editorial: Biomedical Data Visualization: Methods and Applications

Frontiers in Genetics. 2022, 13:890775.

N/A

2022

• T Wu, CL Xiao, TT Lam, G Yu^*

Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection

Frontiers in Microbiology. 2022, 13:723791.

N/A

• X Zhao^#, W Tang^#, H Wan^#, Z Lan H Qin, Q Lin, Y Hu, G Yu^*, N Jiang^*, B Yu^*

Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers

Frontiers in Genetics. 2021, 12:774846.

N/A

2021

• S Xu^#, M Chen^#, T Feng, L Zhan, L Zhou, G Yu^*

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The Innovation. 2021, 2(3):100141.

N/A

• T Wu^#, E Hu^#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo^*, G Yu^*

ggtreeExtra: Compact visualization of richly annotated phylogenetic data

Molecular Biology and Evolution. 2021, 38(9):4039-4042.

N/A

• S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang^*, X Bo^*, G Yu^*

ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram

Frontiers in Genetics. 2021, 12:706907.

N/A

• CH Gao, G Yu, P Cai^*

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures

Frontiers in Immunology. 2021, 12:687975.

N/A

• D Zeng^#, Z Ye^#, R Shen, G Yu, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao^*

nCov2019: an R package for studying the COVID-19 coronavirus pandemic

PeerJ. 2021, 9:e11421.

N/A

• T Wu, E Hu, X Ge^*, G Yu**^*

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

F1000Research. 2021, 9:1246.

N/A

• R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu, SC Hicks, MD Robinson^*

Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment

Frontiers in Genetics. 2021, 12: 625236.

N/A

• S Liu, G Yu^*, L Liu^*, X Zou, L Zhou, E Hu, Y Song

A near-complete genome assembly of Catharanthus roseus and insights into its vinblastine biosynthesis and high susceptibility to the Huanglongbing pathogen

Plant Communications. 2023, 4(2):100388.

N/A

2023

• Zhongping Xu^#, Guanying Wang^#, Qiongqiong Wang, Xiaoting Li, Guangyu Zhang, Ali Qurban, Can Zhang, Yi Zhou, Huan Si, Lisong Hu, Fuqiu Wang, Ying Wang, Zhitao Tian, Wei Chen, Shuangxia Jin^*, Fang Ding^*

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis

Aging (Albany NY). 2020, 12(9):8583-8604.

N/A

2020

• J He^#, S Xu^#, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng^*, G Yu^*, J Chen^*

Using ggtree to Visualize Data on Tree-Like Structure

Current Protocols in Bioinformatics, 69(1):e96

N/A

• G Yu^*

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution. 2020, 37(2):599-603.

N/A

• LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu^*
• Impact Factor = 16.24
• ESI Highly Cited Paper

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

PeerJ Computer Science. 2020, 6:e251.

N/A

• Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu^*, J Chen^*
• ESI Highly Cited Paper

The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Plant Biotechnology Journal, 2022, 21: 78-96.

N/A

2022

• Lisong Hu^#, Zhongping Xu^#, Rui Fan^#, Guanying Wang, Fuqiu Wang, Xiaowei Qin, Lin Yan, Xunzhi Ji, Minghui Meng, Soonliang Sim, Wei Chen, Chaoyun Hao^*, Qinghuang Wang^*, Huaguo Zhu, Shu Zhu^*, Pan Xu^*, Hui Zhao^*, Keith Lindsey, Henry Daniell, Jonathan F. Wendel, Shuangxia Jin^*

Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single-cell transcriptome landscape

Plant Biotechnology Journal, 2021.

N/A

2021

• Zhongping Xu, Qiongqiong Wang, Xiangqian Zhu, Guanying Wang, Yuan Qin, Fang Ding, Lili Tu, Henry Daniell, Xianlong Zhang, Shuangxia Jin^*

The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

Nature Communications. 2019, 10, 4702.

N/A

2022

• Lisong Hu^#, Zhongping Xu^#, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A Saski, Henry Daniell, Jonathan F. Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao^*, Shuangxia Jin^*

Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells

Frontiers in Oncology. 2022, 12:912694.

N/A

• T Feng^#, T Wu^#, Y Zhang^#, L Zhou^#, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang^*, X Shang^*, G Yu^*

ggmsa: a visual exploration tool for multiple sequence alignment and associated data

Briefings in Bioinformatics. 2022, 23(4):bbac222.

N/A

• L Zhou^#, T Feng^#, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai^*, G Yu^*

CBNplot: Bayesian network plots for enrichment analysis

Bioinformatics. 2022, 38(10):2959-2960.

N/A

• N Sato, Y Tamada, G Yu, Y Okuno^*

整合先验知识的单细胞分析策略

首届TICSSO国际单细胞及空间组学大会, Apr 2023

Guangzhou, CN

2023

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The 7^th National Conference on Computational Biology and Bioinformatics

Yantai, CN

2021

Data integration and visualization of phylogenetic trees

BioC Asia, Oct 2020

Virtual Conference

2020

R语言在生物信息学数据可视化中的应用

第八届南方医院博士论坛 - 研而有信之修“生”养“信”, Oct 2019

Southern Medical University

2019

Data integration and visualization of phylogenetic trees

Managing Zoonotic Infections in the era of One Health, Oct 2019

Guangzhou Medical University

R包开发十条建议

第一届生信人才发展论坛

Zhuhai, CN

Two methods for mapping and visualizing associated data on phylogeny using ggtree

第一届南方医科大学基础医学学术年会, Jan 2019

Southern Medical University

ggtree for tree visualization & annotation

Phylogenetic tree visualization workshop/hackathon, May 2017

The Field Museum of Natural History

2017

Computational Methods in Ecology and Evolution

The Second International Workshop on Environmental Microbiomes, Apr 2017

Sun Yat-sen University

R语言与生物信息学

潮博沙龙

Guangzhou, CN

2016

ggtree for visualization and annotation of phylogenetic trees

The 9^th China-R Conference, May 2016

Renmin University of China

iMeta

Associate Editor

N/A

present - 2022

The Innovation

Youth Editor

N/A

南方医科大学基础医学院第二届学术分委员会

委员

N/A

中国生物工程学会

计算生物学与生物信息学专业委员会委员

N/A

present - 2021

广东省精准医学应用学会

微生态医学分会常务委员

Guangdong, CN

present - 2020

广东省医学会

医学遗传学分会青年委员会副主任委员

Guangdong, CN

中国计算机学会

会员

N/A

present - 2019

香港大学校友会

会员

N/A

present - 2017

广东潮博智库

专家

Guangdong, CN

present - 2014

广东省生物信息学会

理事

N/A

2028 - 2023

International Society for Influenza and other Respiratory Virus Disease

Member

N/A

2016

International Network for Data Analysis

Steering Committee

Institut Pasteur

2015